Research workbench

Crystal structure of asfvpolx in complex with DNA enzyme.

Analyse Crystal structure of asfvpolx in complex with DNA enzyme. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XM9
Type: protein + DNA
Length: 814 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Repair DNA polymerase X; DNA (36-mer); DNA (23-mer)
EC: 2.7.7.7
UniProt: P42494
Pockets: 15 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Repair DNA polymerase X (EC 2.7.7.7)	protein	174	32% helix, 32% strand	P42494
E, G	DNA (36-mer)	dna	36	—	—
F, H	DNA (23-mer)	dna	23	—	—

Pockets

15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.69	0.98	18	empty
2	56	0.68	0.96	18	empty
3	288	0.56	0.77	37	empty
4	191	0.50	0.77	24	empty
5	306	0.48	0.72	28	empty

Interfaces

14 interfaces between chains.

G–H · 1175 Å² buried · 110 hydrogen bonds · nucleic-nucleic
E–F · 1166 Å² buried · 105 hydrogen bonds · nucleic-nucleic
A–E · 677 Å² buried · 15 hydrogen bonds · protein-nucleic
C–G · 595 Å² buried · 13 hydrogen bonds · protein-nucleic
B–F · 569 Å² buried · 18 hydrogen bonds · protein-nucleic

Compared structures

5XM9 · Crystal structure of AsfvPolX in complex with DNA enzyme. · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P42494
Elsewhere: RCSB PDB 5XM9 · PDBe 5XM9 · UniProt P42494

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.